Editing PatternQuery:Atlas

{{TOC limit|2}}
=DNA=
=RNA=
==RNA kink-turn motif (Kt-7)==
[[Image:PatternQuery-Atlas-Kt-7.png|200px|thumb|left|Example from ''1ffk'' protein.]]

===PQ expression===
<syntaxhighlight lang="python">
 Near(4, 
  RegularMotifs(’GGCGAAGAAC’, Type=’Nucleotide’), 
  RegularMotifs(’GGGAGCC’, Type=’Nucleotide’)) 
</syntaxhighlight>

<br style="clear:both" />

<code>
Some description goes here
</code>

<br style="clear:both" />


=Protein=
==C<sub>2</sub>H<sub>2</sub> Zinc finger==

[[Image:PatternQuery-Atlas-C2H2.png|200px|thumb|left|Example from ''4r2a'' protein.]]

===PQ expression===
<syntaxhighlight lang="python">
RegularMotifs('.{2}C.{2,4}C.{12}H.{3,5}H').
	  ConnectedAtoms(1).
	  Filter(lambda m:
	    m.Find(Atoms('Zn').
              ConnectedResidues(1).
              Filter(lambda n: 
			(n.Count(Residues('Cys')) == 2) & (n.Count(Residues('His')) == 2))).
		SeqCount() > 0)
</syntaxhighlight>

<br style="clear:both" />

The classical C<sub>2</sub>H<sub>2</sub> zinc finger domain is composed of a simple ββα fold, which is stabilized by a zinc ion coordinated by two histidine and two cysteine residues. The fold is often described by the pattern of X<sub>2</sub>-C-X<sub>2-4</sub>-C-X<sub>12</sub>-H-X<sub>3-5</sub>-H, where X stands for any amino acid, C is cysteine and H is histidine.


==Rubredoxin binding site==
[[Image:PatternQuery-Rubredoxin.png|200px|thumb|right|Example from ''1b13'' protein.]]

===PQ expression===
<syntaxhighlight lang="python">
Atoms("Fe").AmbientResidues(2.5).Filter(lambda l: l.Count(Residues("Cys")) == 4)
</syntaxhighlight>

<br style="clear:both" />

Rubredoxin active site contains an iron ion which is coordinated by the sulfurs of four conserved cysteine residues forming an almost regular tetrahedron. PQ expression identifies Fe atom coordinated by 4 cysteins.



==PA-IIL lectin binding site==
[[Image:PatternQuery-Intro1.png|200px|thumb|left|Example from ''1gzt'' protein.]]

===PQ expression===
<syntaxhighlight lang="python">
	
Near(4, Atoms("Ca"), Atoms("Ca"))
  .ConnectedResidues(1)
  .Filter(lambda l:
    l.Count(Or(Rings(5 * ["C"] + ["O"]), Rings(4 * ["C"] + ["O"]))) > 0)
  .Filter(lambda l: l.Count(Atoms("P")) == 0)
</syntaxhighlight>

<br style="clear:both" />


The PQ expression searches for 2 calcium ions at most 4Å apart, and all the residues with direct interaction with either of these ions. Furthermore, just the molecular patterns containing a residue with a furan or pyran ring were preserved. Additionally, nucleotides are filtered out as well.